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Protein

PHD finger-like domain-containing protein 5A

Gene

Phf5a

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

Functioni

Involved with the PAF1 complex (PAF1C) in transcriptional elongation by RNA polymerase II, and in regulation of development and maintenance of embryonic stem cell (ESC) pluripotency. Required for maintenance of ESCs self-renewal and cellular reprogramming of stem cells. Maintains pluripotency by recruiting and stabilizing PAF1C on pluripotency genes loci, and by regulating the expression of the pluripotency genes. Regulates the deposition of elongation-associated histone modifications, including dimethylated histone H3 'Lys-79' (H3K79me2) and trimethylated histone H3 'Lys-36' (H3K36me3), on PAF1C targets, self-renewal and pluripotency genes. Regulates RNA polymerase II promoter-proximal pause release of the PAF1C targets and self-renewal genes, and the levels of elongating ('Ser-2' phosphorylated) RNA polymerase II in their gene bodies. Regulates muscle specification in adult stem cells by stabilizing PAF1C in chromatin to promote myogenic differentiation (By similarity). Involved in pre-mRNA splicing as a component of the splicing factor SF3B complex. SF3B complex is required for 'A' complex assembly formed by the stable binding of U2 snRNP to the branchpoint sequence (BPS) in pre-mRNA. Sequence independent binding of SF3A/SF3B complex upstream of the branch site is essential, it may anchor U2 snRNP to the pre-mRNA (By similarity). Acts as a transcriptional regulator by binding to the GJA1/Cx43 promoter and enhancing its up-regulation by ESR1/ER-alpha (PubMed:12810571).By similarity1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi11Zinc 1By similarity1
Metal bindingi23Zinc 2By similarity1
Metal bindingi26Zinc 2By similarity1
Metal bindingi30Zinc 3By similarity1
Metal bindingi33Zinc 3By similarity1
Metal bindingi46Zinc 1By similarity1
Metal bindingi49Zinc 1By similarity1
Metal bindingi58Zinc 2By similarity1
Metal bindingi61Zinc 2By similarity1
Metal bindingi72Zinc 3By similarity1
Metal bindingi75Zinc 3By similarity1
Metal bindingi85Zinc 1By similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, RNA-binding
Biological processmRNA processing, mRNA splicing, Transcription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-RNO-72163 mRNA Splicing - Major Pathway

Names & Taxonomyi

Protein namesi
Recommended name:
PHD finger-like domain-containing protein 5A
Short name:
PHD finger-like domain protein 5A
Alternative name(s):
Splicing factor 3B-associated 14 kDa protein
Short name:
SF3b14b
Gene namesi
Name:Phf5a
Synonyms:Ini
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 7

Organism-specific databases

RGDi621555 Phf5a

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00002187182 – 110PHD finger-like domain-containing protein 5AAdd BLAST109

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineBy similarity1
Modified residuei3N6-acetyllysineBy similarity1
Modified residuei94PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

PaxDbiP83871
PRIDEiP83871

PTM databases

iPTMnetiP83871
PhosphoSitePlusiP83871

Expressioni

Tissue specificityi

Expressed in all tissues tested including brain, heart, ovary, uterus, skeletal muscle and testis.1 Publication

Inductioni

By estrogen.1 Publication

Gene expression databases

BgeeiENSRNOG00000024170
ExpressionAtlasiP83871 baseline and differential
GenevisibleiP83871 RN

Interactioni

Subunit structurei

Interacts (via N-terminus) with U2AF1 and SRSF5; acts to bridge the two. Interacts (via C-terminus) with EP400 and DDX1; acts to bridge the two (By similarity). Component of splicing factor SF3B complex which is composed of at least eight subunits; SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6, PHF5A and DDX42. Within the SF3B complex interacts directly with SF3B1 and SF3B3. The SF3B complex composed of SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6 and PHF5A interacts with U2AF2. SF3B associates with the splicing factor SF3A and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex (U2 snRNP). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (By similarity). Interacts with the PAF1 complex (PAF1C) composed of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61. Within the PAF1C interacts directly with CDC73 and WDR61. Interacts with RNA polymerase II (By similarity).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei17Interaction with SF3B3By similarity1
Sitei100Interaction with RNABy similarity1

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000005837

Structurei

3D structure databases

ProteinModelPortaliP83871
SMRiP83871
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni35 – 51Interaction with SF3B1 AND SF3B3By similarityAdd BLAST17
Regioni79 – 82Interaction with SF3B3By similarity4

Sequence similaritiesi

Belongs to the PHF5 family.Curated

Phylogenomic databases

eggNOGiKOG1705 Eukaryota
ENOG4111JIM LUCA
GeneTreeiENSGT00390000018518
HOGENOMiHOG000168285
HOVERGENiHBG053587
InParanoidiP83871
KOiK12834
OMAiYCKECTV
OrthoDBiEOG091G0W8V
PhylomeDBiP83871
TreeFamiTF105627

Family and domain databases

InterProiView protein in InterPro
IPR005345 PHF5
PANTHERiPTHR13120 PTHR13120, 1 hit
PfamiView protein in Pfam
PF03660 PHF5, 1 hit
PIRSFiPIRSF016468 PHF5, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P83871-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKHHPDLIF CRKQAGVAIG RLCEKCDGKC VICDSYVRPC TLVRICDECN
60 70 80 90 100
YGSYQGRCVI CGGPGVSDAY YCKECTIQEK DRDGCPKIVN LGSSKTDLFY
110
ERKKYGFKKR
Length:110
Mass (Da):12,405
Last modified:April 26, 2004 - v1
Checksum:i90F7469DE7292BF7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF495522 mRNA Translation: AAM14623.1
RefSeqiNP_620243.1, NM_138888.1
UniGeneiRn.9116

Genome annotation databases

EnsembliENSRNOT00000005837; ENSRNOP00000005837; ENSRNOG00000024170
GeneIDi192246
KEGGirno:192246
UCSCiRGD:621555 rat

Similar proteinsi

Entry informationi

Entry nameiPHF5A_RAT
AccessioniPrimary (citable) accession number: P83871
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 26, 2004
Last sequence update: April 26, 2004
Last modified: March 28, 2018
This is version 108 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health